YY, I don't know if it's a gene as such but the idea of a spelling "gene" is absolutely true to me.
I think what it is is whether you read words as a whole, which is how most people over 20 were taught to read, or whether you decode phonically. Some people figure that out without ever being taught it, almost instinctively, and it makes it easy to spell. Apparently those of us who do this under the old reading system would have been seen as fast learners and learned to read very quickly, this is simply because rather than having to build up a vocabulary of recognisable words which is a longer process, we built up a set of rules similar to the phonics rules which are now taught explicitly to children. I actually remember learning to read, which according to my school records I did at four, and it seeming to just unlock all of a sudden all at once. So presumably I must have done this (I don't remember though and I'm sure I am just lucky!)
Some misspellings leave me completely baffled as to how the author came up with them, because to me that combination of letters could not, or would be very unlikely to make that sound. And effect / affect is not something I have ever struggled with, because effect can be pronounced as uh-fect or if-fect, and if-fect could never be spelled "affect". Affect can be pronounced as uh-fect or aff-fect, and aff-ect could not be spelt "effect". So I simply run the sentence in my brain with Aff-ect or iff-ect and I know immediately which one to use. But many people do struggle with this one, because of the uh-fect pronunciation which could reasonably be spelt either way.
Have you ever come across the riddle/joke where somebody explains how confusing English spelling is by spelling "fish" "ghoti" ?
They explain that it is like taking the gh from enough, the o from women and the ti from motion.
But this isn't actually how spelling works, the gh sound for example never appears at the beginning of a word and ti doesn't exist as a "sh" sound on its own, it's only ever a combination with "tion".
(Yes I am very boring at parties)